docs: def _generate_tree_log_file(self, tree, alignment, output_tree_file_path,
                                 output_log_file_path, residue_type, fasttree):
          '''Generate the FastTree log file given a tree and the alignment that
          made that tree
  
          Returns
          -------
          Nothing. The log file as parameter is written as the log file.
          '''
          if residue_type==Create._NUCLEOTIDE_PACKAGE_TYPE:
              cmd = "%s -quiet -gtr -nt -nome -mllen -intree '%s' -log %s -out %s %s" %\
                                         (fasttree, tree, output_log_file_path,
                                          output_tree_file_path, alignment)
          elif residue_type==Create._PROTEIN_PACKAGE_TYPE:
              cmd = "%s -quiet -nome -mllen -intree '%s' -log %s -out %s %s" %\
                                         (fasttree, tree, output_log_file_path,
                                          output_tree_file_path, alignment)
          extern.run(cmd)